Stem cell transplantation in the central nervous system (CNS) is currently under intensive investigation as a novel therapeutic approach for a variety of brain disorders and/or injuries. However, one of the main hurdles at the moment is the lack of standardized procedures to evaluate cell graft survival and behavior following transplantation into CNS tissue, thereby leading to the publication of confusing and/or conflicting research results. In this chapter, we therefore provide validated in vivo bioluminescence and postmortem histological procedures to quantitatively determine: (a) the survival of grafted stem cells, and (b) the microglial and astroglial cell responses following cell grafting.